1
|
Baraldo N, Buzzoni L, Pasti L, Cavazzini A, Marchetti N, Mancia A. miRNAs as Biomolecular Markers for Food Safety, Quality, and Traceability in Poultry Meat-A Preliminary Study. Molecules 2024; 29:748. [PMID: 38398499 PMCID: PMC10891583 DOI: 10.3390/molecules29040748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, the expression and abundance of two candidate chicken (Gallus gallus; gga) microRNAs (miRNAs, miR), gga-miR-21-5p (miR-21) and gga-miR-126-5p (miR-126), have been analyzed in order to identify biomarkers for the traceability and quality of poultry meat. Two breeds of broiler chickens were tested: the most common Ross308 (fast-growing) and the high-quality Ranger Gold (slow-growing). A preliminary analysis of the two miRNAs expressions was conducted across various tissues (liver, lung, spleen, skeletal muscle, and kidney), and the three tissues (lung, spleen, and muscle) with a higher expression were chosen for further analysis. Using quantitative reverse transcription polymerase chain reaction (RT-qPCR), the expression of miRNAs in the three tissues of a total of thirteen animals was determined. The results indicate that miR-126 could be a promising biomarker for the lung tissue in the Ranger Gold (RG) breed (p < 0.01), thus suggesting a potential applicability for tracing hybrids. RG exhibits a significantly higher miR-126 expression in the lung tissue compared to the Ross308 broilers (R308), an indication of greater respiratory capacity and, consequently, a higher oxidative metabolism of the fast-growing hybrid. During sampling, two R308 broilers presented some anomalies, including airsacculitis, hepatic steatosis, and enlarged spleen. The expression of miR-126 and miR-21 was compared in healthy animals and in those presenting anomalies. Chickens with airsacculitis and hepatic steatosis showed an up-regulation of miR-21 and miR-126 in the most commercially valuable tissue, the skeletal muscle or breast (p < 0.05).
Collapse
Affiliation(s)
- Nada Baraldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
| | - Luna Buzzoni
- Department of Life Science and Biotechnologies, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
| | - Luisa Pasti
- Department of Environmental and Prevention Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
| | - Alberto Cavazzini
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
- Council for Agricultural Research and Economics, via della Navicella 2/4, 00184 Rome, Italy
| | - Nicola Marchetti
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DoCPAS), University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.C.)
| | - Annalaura Mancia
- Department of Life Science and Biotechnologies, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy;
- Department of Biology and Marine Science, Marine Science Research Institute, 2800 University Blvd N, Jacksonville, FL 32211, USA
| |
Collapse
|
2
|
Andelic M, Marchi M, Marcuzzo S, Lombardi R, Faber CG, Lauria G, Salvi E. Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations. Mol Ther Methods Clin Dev 2023; 31:101116. [PMID: 37808256 PMCID: PMC10550798 DOI: 10.1016/j.omtm.2023.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023]
Abstract
Archived specimens, taken by standardized procedures in clinical practice, represent a valuable resource in translational medicine. Their use in retrospective molecular-based studies could provide disease and therapy predictors. Microfluidic array is a user-friendly and cost-effective method allowing profiling of hundreds of microRNAs (miRNAs) from a low amount of RNA. However, even though tissue miRNAs may include potentially robust biomarkers, non-uniformed post-analytical pipelines could hinder translation into clinics. In this study, epidermal RNA from archival skin biopsy specimens was isolated from patients with peripheral neuropathy and healthy individuals. Unbiased miRNA profiling was performed using RT-qPCR-based microfluidic array. We demonstrated that RNA obtained from archival tissue is appropriate for miRNA profiling, providing evidence that different practices in threshold selection could significantly influence the final results. We showed the utility of software-based quality control for amplification curves. We revealed that selection of the most stable reference and the calculation of geometric mean are suitable when utilizing microfluidic arrays without known references. By applying appropriate post-analytical settings, we obtained miRNA profile of human epidermis associated with biological processes and a list of suitable references. Our results, which outline technical and post-analytical considerations, support the broad use of archived specimens for miRNA analysis to unravel disease-specific molecular signatures.
Collapse
Affiliation(s)
- Mirna Andelic
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- School of Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Margherita Marchi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Stefania Marcuzzo
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Raffaella Lombardi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Catharina G. Faber
- Department of Neurology and School for Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Data Science Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| |
Collapse
|
3
|
dos Santos Bronel BA, Anauate AC, Maquigussa E, Boim MA, da Silva Novaes A. Determination of reference genes as a quantitative standard for gene expression analysis in mouse mesangial cells stimulated with TGF-β. Sci Rep 2022; 12:15626. [PMID: 36115882 PMCID: PMC9482652 DOI: 10.1038/s41598-022-19548-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard technique for gene expression analysis, but the choice of quantitative reference genes (housekeeping genes, HKG) remains challenging. Identify the best HKG is essential for estimating the expression level of target genes. Therefore, the aim of this study was to determine the best HKG for an in vitro model with mouse mesangial cells (MMCs) stimulated with 5 ng/mL of TGF-β. Five candidates HKG were selected: Actb, Hprt, Gapdh, 18S and Ppia. After quantitative expression, the best combination of these genes was analyzed in silico using six software programs. To validate the results, the best genes were used to normalize the expression levels of fibronectin, vimentin and α-SMA. In silico analysis revealed that Ppia, Gapdh and 18S were the most stable genes between the groups. GenEX software and Spearman's correlation determined Ppia and Gapdh as the best HKG pair, and validation of the HKG by normalizing fibronectin, vimentin and α-SMA were consistent with results from the literature. Our results established the combination of Ppia and Gapdh as the best HKG pair for gene expression analysis by RT-PCR in this in vitro model using MMCs treated with TGF-β.
Collapse
|
4
|
Vetrivel S, Zhang R, Engel M, Oßwald A, Watts D, Chen A, Wielockx B, Sbiera S, Reincke M, Riester A. Characterization of Adrenal miRNA-Based Dysregulations in Cushing's Syndrome. Int J Mol Sci 2022; 23:ijms23147676. [PMID: 35887024 PMCID: PMC9320303 DOI: 10.3390/ijms23147676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 02/05/2023] Open
Abstract
MiRNAs are important epigenetic players with tissue- and disease-specific effects. In this study, our aim was to investigate the putative differential expression of miRNAs in adrenal tissues from different forms of Cushing’s syndrome (CS). For this, miRNA-based next-generation sequencing was performed in adrenal tissues taken from patients with ACTH-independent cortisol-producing adrenocortical adenomas (CPA), from patients with ACTH-dependent pituitary Cushing’s disease (CD) after bilateral adrenalectomy, and from control subjects. A confirmatory QPCR was also performed in adrenals from patients with other CS subtypes, such as primary bilateral macronodular hyperplasia and ectopic CS. Sequencing revealed significant differences in the miRNA profiles of CD and CPA. QPCR revealed the upregulated expression of miR-1247-5p in CPA and PBMAH (log2 fold change > 2.5, p < 0.05). MiR-379-5p was found to be upregulated in PBMAH and CD (log2 fold change > 1.8, p < 0.05). Analyses of miR-1247-5p and miR-379-5p expression in the adrenals of mice which had been exposed to short-term ACTH stimulation showed no influence on the adrenal miRNA expression profiles. For miRNA-specific target prediction, RNA-seq data from the adrenals of CPA, PBMAH, and control samples were analyzed with different bioinformatic platforms. The analyses revealed that both miR-1247-5p and miR-379-5p target specific genes in the WNT signaling pathway. In conclusion, this study identified distinct adrenal miRNAs as being associated with CS subtypes.
Collapse
Affiliation(s)
- Sharmilee Vetrivel
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Ru Zhang
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
| | - Andrea Oßwald
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Deepika Watts
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Silviu Sbiera
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany;
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
- Correspondence: ; Tel.: +49-89-440052111
| |
Collapse
|
5
|
Ppia is the most stable housekeeping gene for qRT-PCR normalization in kidneys of three Pkd1-deficient mouse models. Sci Rep 2021; 11:19798. [PMID: 34611276 PMCID: PMC8492864 DOI: 10.1038/s41598-021-99366-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited renal disorder, characterized by renal cyst development leading to end-stage renal disease. Although the appropriate choice of suitable reference is critical for quantitative RNA analysis, no comparison of frequently used “housekeeping” genes is available. Here, we determined the validity of 7 candidate housekeeping genes (Actb, Actg1, B2m, Gapdh, Hprt, Pgam1 and Ppia) in kidney tissues from mouse models orthologous to ADPKD, including a cystic mice (CY) 10–12 weeks old (Pkd1flox/flox:Nestincre/Pkd1flox/−:Nestincre, n = 10) and non-cystic (NC) controls (Pkd1flox/flox/Pkd1flox/-, n = 10), Pkd1-haploinsufficient (HT) mice (Pkd1+/−, n = 6) and wild-type (WT) controls (Pkd1+/+, n = 6) and a severely cystic (SC) mice 15 days old (Pkd1V/V, n = 7) and their controls (CO, n = 5). Gene expression data were analyzed using six distinct statistical softwares. The estimation of the ideal number of genes suggested the use of Ppia alone as sufficient, although not ideal, to analyze groups altogether. Actb, Hprt and Ppia expression profiles were correlated in all samples. Ppia was identified as the most stable housekeeping gene, while Gapdh was the least stable for all kidney samples. Stat3 expression level was consistent with upregulation in SC compared to CO when normalized by Ppia expression. In conclusion, present findings identified Ppia as the best housekeeping gene for CY + NC and SC + CO groups, while Hprt was the best for the HT + WT group.
Collapse
|